Analysis process

Analysis run typeRequiredanalysis_process.analysis_run_type (string enum) Whether the analysis was run or was copied forward as an optimization. Should be one of: "run" or "copy-forward".

Reference filesRequiredanalysis_process.reference_files (array) UUID of the file entities that contain the reference genome used in running the pipeline.

Start timestamp (UTC)Requiredanalysis_process.timestamp_start_utc (string) Initial start time of the full pipeline in UTC. For example "2018-01-21T09:34:27Z".

Stop timestamp (UTC)Requiredanalysis_process.timestamp_stop_utc (string) Terminal stop time of the full pipeline in UTC. For example "2018-01-21T11:35:01Z".

Analysis process>Input parametersRequired (analysis_process array) Input parameters used in the pipeline run.

Checksumanalysis_process.inputs.checksum (string from analysis_process) MD5 checksum of the file. For example "e09a986c2e630130b1849d4bf9a94c06".

Parameter nameRequiredanalysis_process.inputs.parameter_name (string from analysis_process) Name of parameter. For example "stranded" or "rsem_ref_index".

Parameter valueRequiredanalysis_process.inputs.parameter_value (string from analysis_process) Path to file for or value of parameter. For example "NONE" or "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode_v27_primary.tar".

Analysis process>Workflow tasksRequired (analysis_process array) Information about steps in the workflow.

CPUsRequiredanalysis_process.tasks.cpus (integer from analysis_process) Number of CPUs used to run this task. For example "2".

Disk nameRequiredanalysis_process.tasks.disk_size (string from analysis_process) Name of the disk volume mounted to the VM for the task. For example "local-disk 11 HDD".

Docker imageRequiredanalysis_process.tasks.docker_image (string from analysis_process) Name of docker image where the task is stored and executed. For example "quay.io/humancellatlas/secondary-analysis-picard:v0.2.2-2.10.10".

Log erroranalysis_process.tasks.log_err (string from analysis_process) Path where standard error is logged.

Log outanalysis_process.tasks.log_out (string from analysis_process) Path where standard output is logged.

MemoryRequiredanalysis_process.tasks.memory (string from analysis_process) Amount of memory allocated for this task. For example "7.5 GB".

Start timeRequiredanalysis_process.tasks.start_time (string from analysis_process) Date and time when the task started. For example "2019-04-23T20:25:25.969Z".

Stop timeRequiredanalysis_process.tasks.stop_time (string from analysis_process) Date and time when the task finished. For example "2019-04-23T20:28:29.830Z".

Task nameRequiredanalysis_process.tasks.task_name (string from analysis_process) Name of the task. For example "CollectDuplicationMetrics" or "RSEMExpression".

ZoneRequiredanalysis_process.tasks.zone (string from analysis_process) Name of the Google Cloud zone where the task was run. For example "us-central1-b" or "europe-north1-a".

Analysis process>Process typeRequired (process_type_ontology object) The type of process.

Process type ontology IDanalysis_process.type.ontology (string from process_type_ontology) An ontology term identifier in the form prefix:accession. For example "EFO:0009128" or "EFO:0009121".Graph restriction: Subclasses of EFO:0002694 from obo:efo.

Process type ontology labelanalysis_process.type.ontology_label (string from process_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "enzymatic dissociation" or "blood draw".

Process typeRequiredanalysis_process.type.text (string from process_type_ontology) The name of a process type being used. For example "enzymatic dissociation" or "blood draw".

Analysis process>Process coreRequired (process_core object) Core process-level information.

Locationanalysis_process.process_core.location (string from process_core) Location where the process took place. For example "Wellcome Trust Sanger Institute" or "Cancer Institute Stanford University".

Operator(s)analysis_process.process_core.operators (array from process_core) Identifier for individual(s) who executed the process. For example "Technician 1", "JD" or "John Doe".

Process descriptionanalysis_process.process_core.process_description (string from process_core) A general description of the process.

Process IDRequiredanalysis_process.process_core.process_id (string from process_core) A unique ID for the process.

Process nameanalysis_process.process_core.process_name (string from process_core) A short, descriptive name for the process that need not be unique.

Analysis process>provenance (provenance object) Provenance information provided by the system.

Accessionanalysis_process.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredanalysis_process.provenance.document_id (string from provenance) Identifier for document.

Schema major versionanalysis_process.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versionanalysis_process.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredanalysis_process.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDanalysis_process.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update dateanalysis_process.provenance.update_date (string from provenance) When project was last updated.

Updater IDanalysis_process.provenance.updater_id (string from provenance) ID of individual who last updated project.